--- a/build/subconfigure.py
+++ b/build/subconfigure.py
@@ -145,16 +145,20 @@ def split_template(s):
     """Given a "file:template" string, returns "file", "template". If the string
     is of the form "file" (without a template), returns "file", "file.in"."""
     if ':' in s:
         return s.split(':', 1)
     return s, '%s.in' % s
 
 
 def get_config_files(data):
+    # config.status in js/src never contains the output we try to scan here.
+    if data['relobjdir'] == 'js/src':
+        return [], []
+
     config_status = mozpath.join(data['objdir'], 'config.status')
     if not os.path.exists(config_status):
         return [], []
 
     configure = mozpath.join(data['srcdir'], 'configure')
     config_files = []
     command_files = []
 
@@ -261,16 +265,17 @@ def prefix_lines(text, prefix):
 def run(objdir):
     ret = 0
     output = ''
 
     with open(os.path.join(objdir, CONFIGURE_DATA), 'rb') as f:
         data = pickle.load(f)
 
     data['objdir'] = objdir
+    relobjdir = data['relobjdir'] = os.path.relpath(objdir, os.getcwd())
 
     cache_file = data['cache-file']
     cleared_cache = True
     if os.path.exists(cache_file):
         cleared_cache = maybe_clear_cache(data)
 
     config_files, command_files = get_config_files(data)
     contents = []
@@ -298,18 +303,16 @@ def run(objdir):
         config_status = None
     else:
         config_status = File(config_status_path)
         if config_status.mtime < os.path.getmtime(configure) or \
                 data.get('previous-args', data['args']) != data['args'] or \
                 cleared_cache:
             skip_configure = False
 
-    relobjdir = os.path.relpath(objdir, os.getcwd())
-
     if not skip_configure:
         if mozpath.normsep(relobjdir) == 'js/src':
             # Because configure is a shell script calling a python script
             # calling a shell script, on Windows, with msys screwing the
             # environment, we lose the benefits from our own efforts in this
             # script to get past the msys problems. So manually call the python
             # script instead, so that we don't do a native->msys transition
             # here. Then the python configure will still have the right
@@ -347,17 +350,21 @@ def run(objdir):
         if config_status and os.path.getmtime(configure) <= config_status.mtime:
             config_status.update_time()
 
     # Only run config.status if one of the following is true:
     # - config.status changed or did not exist
     # - one of the templates for config files is newer than the corresponding
     #   config file.
     skip_config_status = True
-    if not config_status or config_status.modified:
+    if mozpath.normsep(relobjdir) == 'js/src':
+        # Running config.status in js/src actually does nothing, so we just
+        # skip it.
+        pass
+    elif not config_status or config_status.modified:
         # If config.status doesn't exist after configure (because it's not
         # an autoconf configure), skip it.
         if os.path.exists(config_status_path):
             skip_config_status = False
     else:
         # config.status changed or was created, so we need to update the
         # list of config and command files.
         config_files, command_files = get_config_files(data)